Calibrate association constants to achieve steady states with dissoci…

…ation reactions
KarrLab · Mar 12, 2020 · 2862db5 · 2862db5
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commit 2862db5
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Showing 2 changed files with 15 additions and 7 deletions.
diff --git a/tests/eukaryote/test_complexation.py b/tests/eukaryote/test_complexation.py
@@ -239,10 +239,10 @@ def test_methods(self):
         self.assertEqual(model.parameters.get_one(id='K_m_complex_1_association_in_n_prot3').comments, 
             'The value was assumed to be 1.0 times the concentration of prot3 in nucleus')        
         self.assertEqual(model.parameters.get_one(id='k_cat_complex_1_association_in_n').value, (1/40000 + 2/20000 + 1/25000)/0.1)
-        self.assertEqual(model.parameters.get_one(id='k_cat_complex_1_association_in_n').comments, 
+        self.assertEqual(model.parameters.get_one(id='k_cat_complex_1_association_in_n').comments,
             'The value was assigned so that the ratio of effective dissociation constant to '
             'association constant is the same as the specified ratio of free subunit to subunit in complexes '
-            'at equilibrium')
+            'at equilibrium') 
         self.assertEqual(model.parameters.get_one(id='k_cat_complex_1_dissociation_in_n_degrade_prot1').value, 1/40000.)
         self.assertEqual(model.parameters.get_one(id='k_cat_complex_1_dissociation_in_n_degrade_prot2').value, 2/20000.)
         self.assertEqual(model.parameters.get_one(id='k_cat_complex_1_dissociation_in_n_degrade_prot3').value, 1/25000.)
@@ -268,6 +268,8 @@ def test_methods(self):
         self.assertEqual(model.distribution_init_concentrations.get_one(id='dist-init-conc-complex_2[m]').mean, 9)
         self.assertEqual(model.distribution_init_concentrations.get_one(id='dist-init-conc-complex_2[c_m]').mean, 9)
 
+        self.assertEqual(model.parameters.get_one(id='k_cat_complex_1_association_in_n').value, (1/40000 + 2/20000 + 1/25000) * 4)
+        self.assertEqual(model.parameters.get_one(id='k_cat_complex_2_association_in_n').value, 2/25000 * 2.5)
         self.assertEqual(model.parameters.get_one(id='K_m_complex_1_association_in_n_prot1').value, 6/scipy.constants.Avogadro/5E-14)
         self.assertEqual(model.parameters.get_one(id='K_m_complex_1_association_in_n_prot1').comments, 
             'The value was assumed to be 1.0 times the concentration of prot1 in nucleus')

diff --git a/wc_model_gen/eukaryote/complexation.py b/wc_model_gen/eukaryote/complexation.py
@@ -291,6 +291,8 @@ def calibrate_submodel(self):
                 complex_st_id = reaction.id[:reaction.id.index('_association')]
                 compl_compartment_id = reaction.id[reaction.id.index('_in_') + 4:]
                 compl_compartment = model.compartments.get_one(id=compl_compartment_id)
+                model_compl_species = model.species_types.get_one(
+                    id=complex_st_id).species.get_one(compartment=compl_compartment)
 
                 for param in reaction.rate_laws[0].expression.parameters:
                     if 'K_m_' in param.id:
@@ -312,11 +314,15 @@ def calibrate_submodel(self):
                             param.comments = 'The value was assigned to 1e-05 because the concentration of {} in {} was not known'.format(
                                     species.species_type.id, compl_compartment.name)                    
                     elif 'k_cat_' in param.id:
-                        param.value = self._effective_dissociation_constant['{}[{}]'.format(
-                            complex_st_id, compl_compartment_id)] / subunit_equilibrium_fraction
-                        param.comments = 'The value was assigned so that the ratio of effective dissociation constant to ' + \
-                            'association constant is the same as the specified ratio of free subunit to subunit in complexes ' + \
-                            'at equilibrium'
+                        if model_compl_species.distribution_init_concentration:
+                            param.value = self._effective_dissociation_constant['{}[{}]'.format(
+                                complex_st_id, compl_compartment_id)] * model_compl_species.distribution_init_concentration.mean
+                        else:
+                            param.value = self._effective_dissociation_constant['{}[{}]'.format(
+                                complex_st_id, compl_compartment_id)] / subunit_equilibrium_fraction
+                            param.comments = 'The value was assigned so that the ratio of effective dissociation constant to ' + \
+                                'association constant is the same as the specified ratio of free subunit to subunit in complexes ' + \
+                                'at equilibrium'
 
         print('Complexation submodel has been generated')